So can I pull the things that I'd like to keep, back out of the newly created "RemovedFiles" folder & then install using Apploader so that the items/apps that I took back out of "RemovedFiles" folder WILL be installed?? Does this make sense to anyone else?

You select all the items you would like to remove, click Shrink My OS, anything you wanted removed will be done when you run AppLoader next
All items in RemovedFiles will not be installed and are there for backup purposes and if you would like them restored, you can just put them back in your Java folder
hope that helps